#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 200 ps with a timestep of 1 fs # Temperature 298.15 K # Pressure 1 atm #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 8303 = # of frozen angles find clusters CPU = 0.002 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable npt temp 298.15 298.15 100 iso 1 1 100 drag 0 mtk yes nreset 4000 fix 2 movable ave/time 1 19999 20000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1 fix 3 movable ave/time 20 1 20 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt restart 200000 2.4.restart dump sci all custom 20000 2.4.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32104129 grid = 72 72 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035806992 estimated relative force accuracy = 1.0783169e-05 using double precision KISS FFT 3d grid and FFT values/proc = 23125 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.998003 0.808999 24909 2 95.7868 77.76 8303 Per MPI rank memory allocation (min/avg/max) = 14.39 | 14.82 | 15.37 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 18657.891 400035.3 0.91038687 428.46899 109.25468 1019.0606 0 0 86843.462 283410.92 -936.592 -792155.49 -420772.79 24261.4 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970014 1.45634e-06 24909 2 103.7 0.000108471 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970007 1.65181e-06 24909 2 103.7 0.000120689 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970021 1.38739e-06 24909 2 103.7 0.000100157 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969974 1.22694e-06 24909 2 103.7 0.000100622 8303 200000 200000 227.91731 292119.83 1.2467037 302.43839 137.36188 299.40782 0 0 64050.588 257663.51 -1282.5896 -805388.91 -483238.04 17125.11 Loop time of 3529.86 on 32 procs for 200000 steps with 27300 atoms Performance: 4.895 ns/day, 4.903 hours/ns, 56.659 timesteps/s 98.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1175.5 | 1260.5 | 1406.9 | 164.8 | 35.71 Bond | 0.4603 | 1.1899 | 1.9491 | 32.2 | 0.03 Kspace | 1341.5 | 1488.2 | 1574.1 | 151.2 | 42.16 Neigh | 86.428 | 86.608 | 86.864 | 1.1 | 2.45 Comm | 166.98 | 170.45 | 172.56 | 11.5 | 4.83 Output | 0.022165 | 0.027208 | 0.032041 | 1.8 | 0.00 Modify | 327.49 | 478 | 504.24 | 233.5 | 13.54 Other | | 44.81 | | | 1.27 Nlocal: 853.125 ave 899 max 813 min Histogram: 1 2 3 7 6 5 3 1 3 1 Nghost: 7240.78 ave 7345 max 7122 min Histogram: 1 2 2 6 4 3 3 9 1 1 Neighs: 253625 ave 277601 max 240360 min Histogram: 4 5 5 5 4 5 1 2 0 1 Total # of neighbors = 8116011 Ave neighs/atom = 297.28978 Ave special neighs/atom = 1.892967 Neighbor list builds = 11136 Dangerous builds = 1 undump sci restart 0 dump sci all custom 200000 2.4.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32301495 grid = 64 64 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0037362879 estimated relative force accuracy = 1.125172e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19573 8192 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.969974 1.22694e-06 24909 2 103.7 0.000100622 8303 Per MPI rank memory allocation (min/avg/max) = 14.47 | 14.73 | 15.05 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 200000 200000 74.87011 292119.83 1.2467037 302.43839 137.36188 299.40782 0 0 64050.588 262514.16 -1282.5896 -810239.62 -483238.1 17125.11 Loop time of 7.92997e-06 on 32 procs for 0 steps with 27300 atoms 118.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.93e-06 | | |100.00 Nlocal: 853.125 ave 899 max 813 min Histogram: 1 2 3 7 6 5 3 1 3 1 Nghost: 7240.78 ave 7345 max 7122 min Histogram: 1 2 2 6 4 3 3 9 1 1 Neighs: 253625 ave 277601 max 240360 min Histogram: 4 5 5 5 4 5 1 2 0 1 Total # of neighbors = 8116011 Ave neighs/atom = 297.28978 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out